If I were to use a flannel backing for a quilt, first of all, I would stay with a neutral white or beige and wash a couple of times for shrinkage before actually sewing the backing together and adding it to the quilt. Just my humble opinion, but you would be assured of no fading issues. Also, you can use salt in the water with color flannel to set the color. My Mom used to do that to new jeans when she bought them for us before we were allowed to wear them to prevent the blue denim fading on our underwear.